LOAD_swissprot_blastx: problem with sqlite3

[jules duruz]

Hello!

I am trying to upload my blastx ouput file onto an sqlite database and I get the following error:

CMD: echo "pragma journal_mode=memory;

pragma synchronous=0;

pragma cache_size=4000000;

.mode tabs

.import tmp.blast_bulk_load.28406 BlastDbase" | sqlite3 Trinotate.sqlite

sh: 5: sqlite3: not found

Error, cmd: echo "pragma journal_mode=memory;

pragma synchronous=0;

pragma cache_size=4000000;

.mode tabs

.import tmp.blast_bulk_load.28406 BlastDbase" | sqlite3 Trinotate.sqlite died with ret 32512 at /home/duruzj/workspace/trinotate/Trinotate-Trinotate-v3.1.1/util/trinotateSeqLoader/../../PerlLib/Sqlite_connect.pm line 190, <$fh> line 70066.

Sqlite_connect::bulk_load_sqlite("Trinotate.sqlite", "BlastDbase", "tmp.blast_bulk_load.28406") called at /home/duruzj/workspace/trinotate/Trinotate-Trinotate-v3.1.1/util/trinotateSeqLoader/Trinotate_BLAST_loader.pl line 160

Error, cmd: /home/duruzj/workspace/trinotate/Trinotate-Trinotate-v3.1.1/util/trinotateSeqLoader/Trinotate_BLAST_loader.pl --sqlite Trinotate.sqlite --outfmt6 /home/duruzj/workspace/trinotate/swissprot.blastx.outfmt6 --prog blastx --dbtype Swissprot died with ret 32512 at /home/duruzj/workspace/trinotate/Trinotate-Trinotate-v3.1.1/Trinotate line 126.

The important message here seems to be that sqlite3 can't be found even though I am quite sure it is properly installed. I don't have any experience with this so probably there's something I am missing here... is there any way I should specify sqlite3 location in this function? This wasn't an issue when I did the same thing with TrinotateSeqLoader

Thanks for your help!

Jules

[Brian Haas]

Hi

If you type

   

      which sqlite3

does it provide the path?   If not, then even if it's installed it's not showing up in your PATH setting.  

If you find out where it is, you can add it to your PATH like so:

export PATH=/path/to/sqlite3/containing/directory:${PATH}

best,

~b

 

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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas